Hi Pymol'rs,
I have search the Wiki and Mail-list archive to find a protocul for using
the CMYK color space, but have only found "color-safe" definitions.
My Question(s):
When do you define the color space during the creation of a figure to
ensure usage of a particular color space, ie. cmyk? Can this be done from
a script and with which command, "space cmyk"?
From my understanding from the mail-list, I need to define the color
space before I use any color. Is this correct? Can it also be done
retroactively prior to ray tracing?
Finally, once the color space is defined, do all the rgb colors get
redefined automatically, or does this need to happen manually? I
found the table for the biggest culprits, but Warren pointed out there was
internally defined colors for the atom types. Does someone have a macro
that redefines the pymol defined colors including those for the atoms?
Thanks for your help,
Chris
Christopher L. Colbert, Ph.D.
Research Associate Phone: (214) 645 5944
University of Texas Southwestern Medical Center FAX: (214) 645 5945
6001 Forest Park Lane
Dallas, TX 75390

> I am trying some of pymol scripts from Prof. Robert L. Campbell, which
require cctbx module. but I don't know how to put pymol and cctbx
togther.
> I download window version of cctbx/python2.4 bundle. and I download
pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I
got
> an error message that pymol can't locate python when I tried to install
pymol into site-packages directory. I don't know how to solve this
problem
> since I am new to python scripting. Could anyone give me a hand? Thanks!
There could be a couple of things.
The first thing to check is that the python path (called PYTHONHOME on
unix; not sure about windows) is set up correctly (the executable path may
need adjusting as well, maybe try running with the full path). A
workaround for python path that should work on windows is to add few lines
to the beginning of a python script: import sys (may not be needed if sys
module has already been imported), followed by sys.path.append("full path
to the python/cctbx/pymol modules you want to install).
For python on windows, any compiled modules (which includes parts of cctbx
and pymol) have to be compiled with the same compiler (VisualC++,gcc,
etc), and possible same version, as the python interpreter was complied
with. I'm not sure how you'd go about resolving this, other than hoping
the compiler versions happened to match, or trying to compile both with
the same compiler.
The third possible problem could be that both cctbx and pymol can come
packaged with their own python interpreters (I'm not sure how the windows
executable versions are packaged), so you'll need to make sure that both
are using the same interpreter.
For unix/linux(/os x?), this the fix would be to install everything from
source, and use environmental variables to make sure that pymol knows
about the cctbx packages, and cctbx knows which python to install itself
to. For windows it's likely to be more difficult, if it was me I'd
install cygwin (unix emulator for windows), and just install everything
there.
Hope some of this is helpful,
Pete
Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Thanks a lot. Robert told me the same thing at noon, so I actually did
this for the past few hours, and it never jumped.
One more question, will it be possible to select residues at the
sequence view on the top of the screen without having to drag the
slider, in future builds? (ie. if one have to select more residues than
are displayed, currently one has to select, then drag the slider until
unselected residues come into view, then select and so on. How about the
unselected residues come into view and are selected when the mouse goes
off the view to the left or right?)
Thanks,
Indraneel
On Thu, Aug 18, 2005 at 06:29:19PM -0700, Warren DeLano wrote:
> Indraneel,
>
> When you're in walleye or crosseye stereo mode, try to keep the mouse on
> either the right-hand or left-hand side of the screen. If you cross
> over the center or edge of the window, then you'll get that annoying
> jump.
>
> Fortunately, the problem is eliminated in future builds.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:warren@...
>
>
> > -----Original Message-----
> > From: pymol-users-admin@...
> > [mailto:pymol-users-admin@...] On Behalf Of
> > Indraneel Majumdar
> > Sent: Thursday, August 18, 2005 12:32 PM
> > To: pymol-users@...
> > Subject: [PyMOL] sudden flip / skip / jump while rotating stereo
> >
> > Hi,
> >
> > I could not find anything on this in the archives or google.
> > While rotating a stereo image using the mouse, the molecule
> > suddenly flips back by about 90 degrees. Seems like I get to
> > see only one side of a molecule if rotated on one axis. I can
> > get to see the other side if the molecule is made to do
> > somersaults on all axes, and then I forget what I was looking
> > at. Everything else is normal, but this does hurt an already
> > bulging eyeball. AFAIR this has always been the case (~ last
> > 4 yrs) but I've never had to look at so many structures as
> > I'm doing now... This happens with all types of graphics
> > cards on a i32 debian box.
> >
> > It will really help if someone can let me know what setting
> > to tweak, or even which lines to code to patch.
> >
> > TIA,
> > Indraneel
> >
> > --
> > http://prodata.swmed.edu
> >
> >
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO
> > September 19-22, 2005 * San Francisco, CA * Development
> > Lifecycle Practices
> > Agile & Plan-Driven Development * Managing Projects & Teams *
> > Testing & QA
> > Security * Process Improvement & Measurement *
> > http://www.sqe.com/bsce5sf
> > _______________________________________________
> > PyMOL-users mailing list
> > PyMOL-users@...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
--
http://prodata.swmed.edu

Indraneel,
When you're in walleye or crosseye stereo mode, try to keep the mouse on
either the right-hand or left-hand side of the screen. If you cross
over the center or edge of the window, then you'll get that annoying
jump.
Fortunately, the problem is eliminated in future builds.
Cheers,
Warren
--
Warren L. DeLano, Ph.D. =20
Principal Scientist
. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213 =20
. South San Francisco, CA 94080 USA =20
. Biz:(650)-872-0942 Tech:(650)-872-0834 =20
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:warren@... =20
=20
> -----Original Message-----
> From: pymol-users-admin@...=20
> [mailto:pymol-users-admin@...] On Behalf Of=20
> Indraneel Majumdar
> Sent: Thursday, August 18, 2005 12:32 PM
> To: pymol-users@...
> Subject: [PyMOL] sudden flip / skip / jump while rotating stereo
>=20
> Hi,
>=20
> I could not find anything on this in the archives or google.=20
> While rotating a stereo image using the mouse, the molecule=20
> suddenly flips back by about 90 degrees. Seems like I get to=20
> see only one side of a molecule if rotated on one axis. I can=20
> get to see the other side if the molecule is made to do=20
> somersaults on all axes, and then I forget what I was looking=20
> at. Everything else is normal, but this does hurt an already=20
> bulging eyeball. AFAIR this has always been the case (~ last
> 4 yrs) but I've never had to look at so many structures as=20
> I'm doing now... This happens with all types of graphics=20
> cards on a i32 debian box.
>=20
> It will really help if someone can let me know what setting=20
> to tweak, or even which lines to code to patch.
>=20
> TIA,
> Indraneel
>=20
> --
> http://prodata.swmed.edu
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams *=20
> Testing & QA
> Security * Process Improvement & Measurement *=20
> http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

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